Karen's Daily Blog

Introducing the Wommack Lab

Note: Tomorrow the Microbe section of the website will be up and running, featuring contributions from many of the Extreme 2008 science crew.

My blog today focuses on the work of the Wommack Lab. Dr. Karla Heidelberg, today’s Extreme Blogger, will talk about the work of the Caron Lab and her own lab at the University of Southern California. In the next day or two, look for an Extreme Blog by Lisa Zeigler of Shannon Williamson’s Lab at the J. Craig Venter Institute.

The year was 1989. Dr. K. Eric Wommack was a graduate student at the University of St. Andrews in Scotland when a discovery was made that viruses were extraordinarily abundant in the ocean.

“This completely changed our view of the importance of viral infection and processes – what viruses do in the ocean and their impact on marine ecosystems. Prior to that, they had been believed to be essentially nonexistent in the ocean– a vanishingly insignificant amount,” he says.

A group of scientists working at the University of Bergen, Norway, were working to characterize the composition of bacteria in the the ocean to see what basic elements they were made of. When they looked through the transmission electron microscope, they saw tons of viruses. After the initial discovery, the Norwegian scientists requested water samples from scientists all over the world. They saw lots of viruses.

“This completely changed our perception of the world,” says Eric now.

The key is the interaction between viruses and the bacteria they invade. If you were a burglar who invaded a home, the homeowner wouldn’t be considered your host, a word that connotes some kind of mutual appreciation. But in the case of viruses and bacteria, the idea of host applies, even if the “guest” is an invader, because the linkup seems to be useful and necessary to the bacteria.

The key to understanding this lies in seeing how bacteria benefit the environment. They are the great recyclers, transforming chemicals into useful forms for plants and animals. The nutrient cycles of the major elements, such as carbon and nitrogen, are controlled by and large by bacteria. So what did it mean that so many viruses were discovered? Why is it important that they’re killing the bacteria? What’s the impact of their abundance? It took many years of work before microbiologists were able to estimate that around 20% of bacteria a day are killed by viruses, a number that changes depending on location.

“It could be as high as 100 % or as low as nonexistent,” says Eric.

But they haven’t studied viruses in enough environments to understand the balance between bacteria that produce because of viruses, bacteria that die because of them, and the impact on organisms that eat the bacteria. One goal for researchers is to create a model that shows the potential effects on environments of different levels of viruses and their host bacteria.

Other members of the Wommack Lab have learned that a sample of soil holds 1,000 times more viruses than bacteria. In the sea, the ratio is closer to ten times. What this means for the hydrothermal vent ecosystem, where bacteria form the basis of the food chain, is the key question the Wommack group is trying to get at. Because there is no sunlight here, bacterial processes are especially important in transferring energy to living things.

Eric says, “When bacteria die, the processes they do are impacted.”

Bekki Helton says, “Viruses are the living dead. The only sign they’re alive on their own is that they have DNA.”

It’s true that viruses only live by infecting bacteria cells. Viruses bring genes along that can change the capabilities of their hosts. While this occurs everywhere, the vent microbiologists think there’s a fundamentally different association between viruses and their hosts down here than anywhere else. This relationship is just one thing that makes the hydrothermal vents an extreme environment. It’s a complex topic, these viruses! So the Wommack Lab has created a block of topics and activities to help you get a grip.

“We sat down as a group and hashed out what we thought would be interesting topics, important things for people to know about viruses.“

We’re grateful to them all --- including the lab members that are still on terra firma back home in Delaware. Below, you’ll find a list of who’s who and what’s what. I’d recommend starting with Shawn Polson’s glossary, and moving on in whatever direction interests you. But don’t miss the opportunity to make your own little virus mascot, courtesy of Dr. Danielle Winget.

From left to right: Dr. Eric Wommack, Doug Fadrosh, Bekki Helton, Shawn Polson and Lisa Zeigler.

Today's Extreme Blogger:
Karla Heidelberg

Hydrothermal Vents

Hydrothermal vent systems are an unbelievably exciting system to study. When someone mentions “hydrothermal vents,” many people immediately visualize the dense assemblages of Riftia and Tevnia worms around the hot water and soot that come up through chimneys. While these larger images are visually stunning, my scientific interests are in a much smaller size-fraction of the community -- the single-celled eukaryotic microbes, also known as protists. These organisms, along with the bacteria and archaea, can form the base of the food chain that supports the higher trophic levels. Also, predation by protists not only controls populations of other microbes, but some protists have even evolved symbiotic and parasitic relationships with other protists and larger animals.

 

Studying microbes in these systems is not new, but most previous studies have focused only on bacteria and/or archaea. My graduate student, Amy Koid, and I are working with the other scientists on this cruise to focus on the eukaryotic microbial fraction using new tools and novel approaches. We are pairing molecular approaches -- evaluating DNA and RNA -- with traditional light microscopy to evaluate diversity; seeing different organisms under the scope tells us qualitatively how many different organisms are in the area, while the differences in DNA sequences show genetic differences. We are now on day seven of our work. When the Alvin submarine comes up each evening, it brings a variety of sample types that are loaded with protists. Some organisms are coming from "protist traps" that we set out last year on the bottom in and around the vents for colonization (shown here). Others come from surfaces of bottom organisms, such as Riftia. Like any organism, including humans, Riftia carry a complex layer of microbeds on its surface.

In addition, I have brought a modified environmental scanning electron microscope (eSEM) to sea (the first time, to my knowledge, that an SEM has been out to sea!) to compliment these other approaches. Unlike the more traditional light microscopes, this instrument uses backscattered electrons to produce really detailed images of the surface morphology (appearance or surface structures) of very small organisms.  Live samples can be immediately mounted onto a small metal pedestal and inserted into the eSEM chamber. The air is evacuated out of the chamber, and the sample is bombarded with electrons.

ABOVE: An assemblage of possibly undescribed hydrothermal vent protists. To scientists, the word undescribed connotes a newly discovered organism. The backscattering of the electrons can then be imaged by a computer to show the fine-scale morphology of what each microbe looks like.

The images obtained so far from our eSEM have thus far exceeded our expectations for documenting microbial communities and possibly discovering novel life forms. We are looking forward to pairing these images with the molecular work (analysis of DNA) needed to categorize our samples in several different ways.

 

Every aspect of working on a remote research vessel at sea is a challenge, but there is something truly indescribable about going to sea and working in systems like hydrothermal vent communities. The organisms in these systems are so different than the typical things that we are used to seeing in surface ocean waters, which provides an unbelievable opportunity to discover truly novel ecology. With a little imagination, one organism (right) even looked remarkably similar to the Alvin submarine! It is a great day to be an oceanographer.

Photo Gallery

Video Gallery

Dive Log

Dive 4474 (P.I.T. Dive)                        November 16, 2008                        AT15-39

Pilot: Korey Verhein
Port Observer: Dave Caron
Starboard Co-Pilot: Mark Spear

9˚ North, East Pacific Rise (V Vent area)

GMT 14:13            Cleared surface
GMT 14:30             566 m
GMT 14:45             970 m
GMT 15:00             1415 m
GMT 15:15             1872 m
GMT 15:30             2395 m

GMT 15:35:          On the bottom. Depth 2538 m

GMT 16:07:          Located elevator with LVWS.
GMT 16:25:          Picked up elevator.
GMT 17:45:          Elevator dropped into place on basalt near a small black smoker.  Intake placed at a small
                               crack on bare basalt that had shimmering water emerging from it (temp ≈ 22˚C). 
                               X=5548, Y=72379, Z=2513, heading 23.6.
GMT 17:54            Sipper samples collected (syringes #1 and #2).
GMT 18:01            Turned on LVWS and left site.

GMT 18:45            Located and retrieved protistan colonization array #9 on bare basalt not far from small black                                 smoker.  Temperature (4.4˚C) was noted at location of array prior to retrieval.
                                Sipper samples collected prior to retrieval (syringes #3 and #4).
                                NB: Sipper #5 misfired.  Syringe #5 and #6 were skipped and #7 was used next.

GMT 18:52            Collected approximately 8 mussels from large mussel bed.
                                X= 5537, Y= 72373, Z= 2511.

GMT 19:15           Retrieved protistan colonization array #1 (sponge colonizer and a slide colonizer).  It was
                               deployed within a mussel bed.  Some mussel byssal attachments were noted on the array.
                               Sipper samples collected prior to retrieval (syringes #7 and #8).

GMT 19:30            One clam retrieved, but shell was broken during collection.

GMT 19:35           One protistan colonization array deployed (#116) within the same mussel bed from which the
                               mussels were collected.  The mussels apparently were near a seep area because there were
                               swarms of amphipods are this group of mussels.
                                X=5532, Y=72366, Z= 2507.

GMT 20:08            Seven/eight more clams collected.
                                X=5535, Y=72362, Z= 2506.

GMT 20:11            Three/four more clams collected from a nearby location.
                                X=5535, Y=72364, Z= 2507.

GMT 20:24            Slurp sample (white) collected from among large accumulations of decaying tubes of Tevnia
                               and Riftia.  The tip of the slurp was used to disturb the accumulations and suction up the grunge
                               that was associated with the tube debris.
                                X=5544, Y=72402, Z= 2513.

GMT 20:32            Grab sample of decaying tubes of Tevnia and Riftia, placed in the biobox. 
                                X=5544, Y=72402, Z= 2513.

GMT 20:36            One protistan colonization array deployed (#112) on top of the decaying tubes of Tevnia and
                               Riftia from which the slurp and grab samples were collected.
                                X=5543, Y=72404, Z= 2513.  Heading 273.
                       

GMT 20:39:             Arrived V vent.

GMT 20:52             Temperature probe of Alvinella tubes.
                                Sipper samples collected (syringes #9 and #10).
                                X=5540, Y=72404, Z= 2507.
                                Alvinella worms collected from V vent into Arte chamber #3.  The chamber was then flooded
                               with RNA Later.  Worms and tubes were taken using the Alvin arm to pull tubes and animals.

GMT 21:10            Temperature probe of Alvinella tubes.
                                 Sipper samples collected (syringes #11 and #12).
                                X=5540, Y=72404, Z= 2507.
                                Alvinella worms collected from V vent into Arte chamber #1.  Worms and tubes were suctioned
                               up using the slurp gun, the tubes and worms then spread out onto the top of the closed bioboxes,
                               and the worms teased out and placedin the Arte chamber.  The chamber was then flooded with
                               RNA Later.

GMT 21:15            Alvinella worms collected from V vent into Arte chamber #2.  Worms and tubes were collected
                               and handled as noted above.

GMT 21:35            Moved off site and dropped weights.